static void Main(string[] args)
{
Console.WriteLine("Loading kit names ...");
string curr_dir = "";
//debug
//curr_dir = @"D:\Genetics\Ancient-DNA\";
if (!File.Exists(curr_dir + "atree.txt"))
{
Console.WriteLine("atree.txt does not exist!");
return;
}
string[] lines = null;
string[] data = null;
if (File.Exists(curr_dir + @"ref\kit-names.txt"))
{
lines = File.ReadAllLines(curr_dir + @"ref\kit-names.txt");
foreach (string line in lines)
{
if (line.Trim() == "")
{
continue;
}
data = line.Split(new char[] { ',' });
kitmap.Add(data[0], data[1]);
}
}
//
lines = File.ReadAllLines(curr_dir + "atree.txt");
data = null;
List <CommonAncestor> tree = new List <CommonAncestor>();
foreach (string line in lines)
{
data = line.Split(new char[] { ',' });
CommonAncestor ancestor = new CommonAncestor();
ancestor.name = data[0];
ancestor.id = data[1];
ancestor.kits = new List <string>(data[1].Split(new char[] { '-' }));
ancestor.segments = new List <Segment>();
foreach (string segstr in data[2].Split(new char[] { '_' }))
{
ancestor.segments.Add(new Segment(segstr.Split(new char[] { ':' })));
}
ancestor.descendents = new List <CommonAncestor>();
addToTree(tree, ancestor);
}
string ca_xml = "<CA NAME='ADAM-EVE'>" + drawTree(tree) + "\r\n</CA>";
File.WriteAllText("atree.xml", ca_xml);
Console.WriteLine("atree.xml successfully written.");
}
private static void addToTree(List <CommonAncestor> tree, CommonAncestor ancestor)
{
foreach (CommonAncestor par in tree)
{
if (AncestorKitsPresent(par, ancestor))
{
addToTree(par.descendents, ancestor);
return;
}
}
tree.Add(ancestor);
}
private static bool AncestorKitsPresent(CommonAncestor par,
CommonAncestor ancestor)
{
List <string> pkits = par.kits;
List <string> akits = ancestor.kits;
foreach (string kit in akits)
{
if (!pkits.Contains(kit))
{
return(false);
}
}
return(true);
}
public static void doGenXML()
{
Program.addLog("Loading kit names ...");
string curr_dir = "";
//debug
//curr_dir = @"D:\Genetics\Ancient-DNA\";
if (!File.Exists(curr_dir + "atree.txt"))
{
Program.addLog("atree.txt does not exist!");
return;
}
string[] lines = null;
string[] data = null;
//
lines = File.ReadAllLines(curr_dir + "atree.txt");
data = null;
List <CommonAncestor> tree = new List <CommonAncestor>();
foreach (string line in lines)
{
data = line.Split(new char[] { ',' });
CommonAncestor ancestor = new CommonAncestor();
ancestor.name = data[0];
ancestor.id = data[1];
ancestor.kits = new List <string>(data[1].Split(new char[] { '-' }));
ancestor.segments = new List <Segment>();
foreach (string segstr in data[2].Split(new char[] { '_' }))
{
ancestor.segments.Add(new Segment(segstr.Split(new char[] { ':' })));
}
ancestor.descendents = new List <CommonAncestor>();
addToTree(tree, ancestor);
}
string ca_xml = "<CA NAME='ADAM-EVE'>" + drawTree(tree) + "\r\n</CA>";
File.WriteAllText("atree.xml", ca_xml);
Program.addLog("atree.xml successfully written.");
}